Liphardt Lab


We're a biophysics lab. We investigate biological spatial organization on the mesoscale (10 nm - 10 microns) and the role of mechanical cues in cellular decision-making. Current research directions include tissue mechanobiology, the organization of the DNA inside the nucleus, and single-molecule measurements of transport through biological pores and channels. We also invent and refine tools for precision control and characterization of cells and tissues. Characterization technologies include super-resolution light microscopy. Our lab is located in the Shriram Center at Stanford University.

In addition to 'classical' biophysics, we have been exploring health wearables, IoT, and algorithms; the general challenge is to measure the right thing, and then, figure out how to make sense of that information to prevent, detect, and treat disease. We have begun to use machine-learning, AI, and statistical approaches to interpret information flowing from sensor systems. Finally, to help bring together patients, engineers, computer scientists, and social networking technologists, we co-founded CancerBase.org, a place where patients can share data and learn from one-another.



Major Research Directions: Patterns, Energy, and Information


NPC

Single molecule studies of the Nuclear Pore Complex

In collaboration with Karsten Weis, we are using single-molecule tracking approaches to learn how the NPC controls access to the nucleus. The image shows a schematic of a NPC in the nuclear membrane, and a single cargo transiting the pore. The panel below shows a single cargo being tracked as it translocates the pore. The NPC is both highly selective and efficient; our goal is to understand how the pore implements those apparently conflicting goals. Moreover, we would like to clarify the fundamental basis for the pore's ability to efficiently rectify molecular transport.

Nucleus

Genome-wide coordination of gene expression

Imagine you are an orchestra conductor directing a symphony. If you're good at what you do, everything will sound right. How does the genome solve the equivalent problem, except without a conductor? We use genome-edited cell lines to investigate how DNA-looping and chromatin compaction influence transcriptional regulation. The image above shows a single nucleus. The DNA is blue, single RNA transcripts are red/yellow.

Network

Mechanobiology of multicellular structures

How do multicellular structures interact with biological matrices such as collagen? We use mammary acini as our basic model system. Mammary acini are composed of about 100 cells and are the basic functional and anatomical units of the human breast. We use mammary acini to explore how collections of cells generate mechanical cues and how these cues spread through biological gels, influencing the decisions of other cells and multicellular structures. The image above shows several hundred mammary acini (tiny red dots) deposited on a collagen matrix (green).



Tools for Control and Measurement; Polymers and Forces


Rotating E. coli

Plasmon Rulers

RNA

Nanowires

DNA Loops

Tools and methods. Scroll over the images to learn more.